Merge pull request #517 from dimitri-yatsenko/master

Fix issues #483, #516, and #518

Author: eywalker

CHANGELOG.md

@@ -1,5 +1,9 @@
 ## Release notes
 
+### 0.11.1 -- Nov 15, 2018
+* Fix ordering of attributes in proj (#483 and #516)
+* Prohibit direct insert into auto-populated tables (#511)
+
 ### 0.11.0 -- Oct 25, 2018
 * Full support of dependencies with renamed attributes using projection syntax (#300, #345, #436, #506, #507)
 * Rename internal class and module names to comply with terminology in documentation (#494, #500)

datajoint/__init__.py

@@ -15,11 +15,10 @@
 """
 
 import os
-from types import ModuleType
 from .version import __version__
 
 __author__ = "Dimitri Yatsenko, Edgar Y. Walker, and Fabian Sinz at Baylor College of Medicine"
-__date__ = "Oct 25, 2018"
+__date__ = "Nov 15, 2018"
 __all__ = ['__author__', '__version__',
            'config', 'conn', 'kill', 'Table',
            'Connection', 'Heading', 'FreeTable', 'Not', 'schema',
@@ -68,15 +67,15 @@ class key:
 from .connection import conn, Connection
 from .table import FreeTable, Table
 from .user_tables import Manual, Lookup, Imported, Computed, Part
-from .query import Not, AndList, U
+from .expression import Not, AndList, U
 from .heading import Heading
 from .schema import Schema as schema
 from .erd import ERD
 from .admin import set_password, kill
 from .errors import DataJointError, DuplicateError
 
 
-def create_virtual_module(module_name, schema_name, create_schema=False, create_tables=False):
+def create_virtual_module(module_name, schema_name, create_schema=False, create_tables=False, connection=None):
     """
     Creates a python module with the given name from the name of a schema on the server and
     automatically adds classes to it corresponding to the tables in the schema.
@@ -87,8 +86,9 @@ def create_virtual_module(module_name, schema_name, create_schema=False, create_
     :param create_tables: if True, module.schema can be used as the decorator for declaring new
     :return: the python module containing classes from the schema object and the table classes
     """
-    module = ModuleType(module_name)
-    _schema = schema(schema_name, create_schema=create_schema, create_tables=create_tables)
+    import types
+    module = types.ModuleType(module_name)
+    _schema = schema(schema_name, create_schema=create_schema, create_tables=create_tables, connection=connection)
     _schema.spawn_missing_classes(context=module.__dict__)
     module.__dict__['schema'] = _schema
     return module

datajoint/admin.py

@@ -43,7 +43,8 @@ def kill(restriction=None, connection=None):  # pragma: no cover
     while True:
         print('  ID USER         STATE         TIME  INFO')
         print('+--+ +----------+ +-----------+ +--+')
-        for process in connection.query(query, as_dict=True).fetchall():
+        cur = connection.query(query, as_dict=True)
+        for process in cur:
             try:
                 print('{ID:>4d} {USER:<12s} {STATE:<12s} {TIME:>5d}  {INFO}'.format(**process))
             except TypeError:

datajoint/autopopulate.py

@@ -5,7 +5,7 @@
 import random
 from tqdm import tqdm
 from pymysql import OperationalError
-from .query import Query, AndList, U
+from .expression import QueryExpression, AndList, U
 from .errors import DataJointError
 from .table import FreeTable
 import signal
@@ -84,7 +84,7 @@ def _jobs_to_do(self, restrictions):
             raise DataJointError('Cannot call populate on a restricted table. '
                                  'Instead, pass conditions to populate() as arguments.')
         todo = self.key_source
-        if not isinstance(todo, Query):
+        if not isinstance(todo, QueryExpression):
             raise DataJointError('Invalid key_source value')
         # check if target lacks any attributes from the primary key of key_source
         try:

datajoint/declare.py

@@ -90,7 +90,7 @@ def compile_foreign_key(line, context, attributes, primary_key, attr_sql, foreig
     """
     # Parse and validate
     from .table import Table
-    from .query import Projection
+    from .expression import Projection
 
     new_style = True   # See issue #436.  Old style to be deprecated in a future release
     try:
@@ -194,7 +194,7 @@ def declare(full_table_name, definition, context):
 
     :param full_table_name: full name of the table
     :param definition: DataJoint table definition
-    :param context: dictionary of objects that might be referred to in the table. Usually this will be locals()
+    :param context: dictionary of objects that might be referred to in the table.
     """
     # split definition into lines
     definition = re.split(r'\s*\n\s*', definition.strip())

datajoint/erd.py

@@ -197,31 +197,6 @@ def __mul__(self, arg):
             self.nodes_to_show.intersection_update(arg.nodes_to_show)
             return self
 
-        def topological_sort(self):
-            """
-            :return:  list of nodes in topological order
-            """
-
-            def _unite(lst):
-                """
-                reorder list so that parts immediately follow their masters without breaking the topological order.
-                Without this correction, simple topological sort may insert other descendants between master and parts
-                :example:
-                _unite(['a', 'a__q', 'b', 'c', 'c__q', 'b__q', 'd', 'a__r'])
-                -> ['a', 'a__q', 'a__r', 'b', 'b__q', 'c', 'c__q', 'd']
-                """
-                if len(lst) <= 2:
-                    return lst
-                el = lst.pop()
-                lst = _unite(lst)
-                if '__' in el:
-                    master = el.split('__')[0]
-                    if not lst[-1].startswith(master):
-                        return _unite(lst[:-1] + [el, lst[-1]])
-                return lst + [el]
-
-            return _unite(list(nx.algorithms.dag.topological_sort(self.subgraph(self.nodes_to_show))))
-
         def _make_graph(self):
             """
             Make the self.graph - a graph object ready for drawing